Variant report

Variant	rs12092817
Chromosome Location	chr1:150777707-150777708
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150550459..150552854-chr1:150773382..150778382,4	MCF-7	breast:
2	chr1:150775628..150778806-chr1:150780068..150784511,4	MCF-7	breast:
3	chr1:150668010..150669720-chr1:150777076..150779971,2	MCF-7	breast:
4	chr1:150760391..150762375-chr1:150777172..150778820,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143457	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000143387	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10305652	1.00[EUR][1000 genomes]
rs11799727	1.00[AMR][1000 genomes]
rs11809393	1.00[AMR][1000 genomes]
rs12065659	1.00[AMR][1000 genomes]
rs12075189	1.00[AMR][1000 genomes]
rs12088369	1.00[AMR][1000 genomes]
rs12089548	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12093938	1.00[AMR][1000 genomes]
rs16839661	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs35822171	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12092817	PLA2G16	trans	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150760600-150779600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:150761200-150783200	Weak transcription	GM12878-XiMat	blood
3	chr1:150762400-150779200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:150762400-150780000	Weak transcription	NHEK	skin
5	chr1:150764600-150781600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:150765400-150781400	Weak transcription	HMEC	breast
7	chr1:150765400-150793600	Weak transcription	Fetal Heart	heart
8	chr1:150767000-150779400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:150767200-150779400	Weak transcription	Fetal Brain Male	brain
10	chr1:150767600-150783600	Weak transcription	Psoas Muscle	Psoas
11	chr1:150767800-150778400	Strong transcription	Fetal Muscle Leg	muscle
12	chr1:150767800-150780200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:150768200-150784000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:150769400-150785200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:150770000-150781600	Weak transcription	HSMMtube	muscle
16	chr1:150770400-150778400	Weak transcription	Gastric	stomach
17	chr1:150770400-150783400	Weak transcription	Stomach Mucosa	stomach
18	chr1:150770600-150779200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:150770600-150779600	Weak transcription	Fetal Thymus	thymus
20	chr1:150770600-150783600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:150770800-150780600	Weak transcription	Esophagus	oesophagus
22	chr1:150771200-150784600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:150771200-150785400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:150771400-150783000	Weak transcription	Brain Germinal Matrix	brain
25	chr1:150771600-150785200	Weak transcription	Pancreas	Pancrea
26	chr1:150771800-150778200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:150771800-150779200	Weak transcription	Fetal Lung	lung
28	chr1:150771800-150783600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:150771800-150783600	Weak transcription	A549	lung
30	chr1:150772000-150778400	Weak transcription	Colonic Mucosa	Colon
31	chr1:150772000-150779400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:150772000-150780600	Weak transcription	Fetal Brain Female	brain
33	chr1:150772200-150778200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:150772200-150778400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:150772200-150778400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:150772200-150779000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:150772200-150779000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:150772200-150779000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:150772200-150779000	Weak transcription	Thymus	Thymus
40	chr1:150772200-150779400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:150772200-150779400	Weak transcription	Primary B cells from cord blood	blood
42	chr1:150772200-150779400	Weak transcription	Fetal Kidney	kidney
43	chr1:150772200-150779600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:150772200-150779800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:150772200-150779800	Weak transcription	Brain Anterior Caudate	brain
46	chr1:150772200-150779800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:150772200-150779800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:150772200-150779800	Weak transcription	Fetal Intestine Large	intestine
49	chr1:150772200-150780000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:150772200-150780000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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